Here is how the system works:

On startup, the ECU operates the turbo normally (wastegate closed) and keeps the EGR closed too. Then after one minute it assumes that the EGR is a bit warmed up and tests it by opening and closing it a few times. It checks the movement of the EGR valve with a sensor on the back of the EGR. If the EGR is stuck, it turns off the turbo until the engine is restarted.

Things that can go wrong.
1) No vacuum in system (rare, but hoses do leak or get pulled out)
2) EGR vacuum modulator does not work or is slow (pretty common)
3) EGR sticks (very common)
4) TURBO vacuum modulator does not work or is slow (less common)

I have tried to fix a vacuum modulator. Not successful, even after several tries. Don't waste your time. Test with a known good one before buying.

The EGR can be loosened up with carburetor cleaner and manual cleaning. After you get it working you should think about putting a plug into the big exhaust line. Do not plug the EGR vacuum line. That is the same as causing #2 failure. The engine computer will spot the plug right away.

Note for the US readers: The plug in the exhaust line does not work for the 98 & 99 E300DT. The engine management software is different and this plug will be detected too.